Find research datasets worth reusing

opencc-zeroFeb 2023View details →

Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome

Abstract A compelling interest in marine biology is to elucidate how species boundaries between sympatric free‐spawning marine invertebrates such as bivalve molluscs are maintained in the face of potential hybridization. Hybrid zones provide the natural resources for us to study the underlying genetic mechanisms of reproductive isolation between hybridizing species. Against this backdrop, we examined the occurrence of introgressive hybridization (introgression) between two bivalves distributed in the western Pacific margin, Atrina japonica and Atrina lischkeana, based on single‐nucleotide polymorphisms (SNPs) derived from restriction site‐associated DNA sequencing. Using 1066 ancestry‐informative SNP sites, we also investigated the extent of introgression within the genome to search for SNP sites with reduced interspecies gene flow. A series of our individual‐level clustering analyses including the principal component analysis, Bayesian model‐based clustering, and triangle plotting based on ancestry–heterozygosity relationships for an admixed population sample from the Seto Inland Sea (Japan) consistently suggested the presence of specimens with varying degrees of genomic admixture, thereby implying that the two species are not completely isolated. The Bayesian genomic cline analysis identified 10 SNP sites with reduced introgression, each of which was located within a genic region or an intergenic region physically close to a functional gene. No, or very few, heterozygotes were observed at these sites in the hybrid zone, suggesting that selection acts against heterozygotes. Accordingly, we raised the possibility that the SNP sites are within genomic regions that are incompatible between the two species. Our finding of restricted interspecies gene flow at certain genomic regions gives new insight into the maintenance of species boundaries in hybridizing broadcast‐spawning molluscs.

opencc-zeroDec 2022View details →

Supporting information for: The correct name for an Aquilegia (Ranunculaceae) hybrid of the parentage Aquilegia flavescens × A. formosa

Aquilegia x miniana (J.F.Macbr. & Payson) Cronk, hybr. & stat. nov. is the correct name for the hybrid Aquilegia flavescens S.Watson x A. formosa Fisch. ex DC. var. formosa. In 1916, Payson and Macbride, while exploring the mountains of Idaho, found populations of Aquilegia that were pink in flower colour and appeared intermediate between the yellow-flowered A. flavescens and red-flowered A. formosa. They named these plants A. flavescens var. miniana J.F.Macbr. & Payson. There has been uncertainty over whether their type collections (in GH, RM, MO, US, E, CM, CAS, NY) do indeed represent hybrids or pink-flowered morphs of A. flavescens. Using a Wells diagram, the holotype (in the Gray Herbarium of Harvard University) is shown to be intermediate, allowing its identification as a clear hybrid. However, some of the isotype material is indistinguishable from A. flavescens. The holotype matches material from British Columbia that has been determined as being of hybrid origin using molecular and morphological data. A. flavescens var. miniana J.F.Macbr. & Payson is, therefore, an available name for the hybrid, which is here raised to the status of hybrid binomial.

opencc-by-4.0Mar 2023View details →

Simulation dataset of "Wave activities throughout a low-Mach number quasi-parallel shock: 2-D hybrid simulations"

Simulation dataset of "Wave activities throughout a low-Mach number quasi-parallel shock: 2-D hybrid simulations", including magnetic fields, number density and average velocities of particles.

opencc-zeroMar 2023View details →

Data from: Differential gene expression and mitonuclear incompatibilities in fast- and slow-developing inter-population Tigriopus californicus hybrids

Mitochondrial functions are intimately reliant on proteins and RNAs encoded in both the nuclear and mitochondrial genomes, leading to inter-genomic coevolution within taxa. Hybridization can break apart coevolved mitonuclear genotypes, resulting in decreased mitochondrial performance and reduced fitness. This hybrid breakdown is an important component of outbreeding depression and early-stage reproductive isolation. However, the mechanisms contributing to mitonuclear interactions remain poorly resolved. Here we scored variation in developmental rate (a proxy for fitness) among reciprocal F2 inter-population hybrids of the intertidal copepod Tigriopus californicus, and used RNA sequencing to assess differences in gene expression between fast- and slow-developing hybrids. In total, differences in expression associated with developmental rate were detected for 2,925 genes, whereas only 135 genes were differentially expressed as a result of differences in mitochondrial genotype. Up-regulated expression in fast developers was enriched for genes involved in chitin-based cuticle development, oxidation-reduction processes, hydrogen peroxide catabolic processes, and mitochondrial respiratory chain complex I. In contrast, up-regulation in slow developers was enriched for DNA replication, cell division, DNA damage, and DNA repair. Eighty-four nuclear-encoded mitochondrial genes were differentially expressed between fast- and slow-developing copepods, including twelve subunits of the electron transport system (ETS) which all had higher expression in fast developers than in slow developers. Nine of these genes were subunits of ETS complex I. Our results emphasize the major roles that mitonuclear interactions within the ETS, particularly in complex I, play in hybrid breakdown, and resolve strong candidate genes for involvement in mitonuclear interactions.

opencc-by-4.0Mar 2023View details →

# Blocks? Graphs? Why Not Both? Designing and Evaluating a Hybrid Programming Environment for End-users: Replication Package

Blocks? Graphs? Why Not Both? Designing and Evaluating a Hybrid Programming Environment for End-users: Replication Package This repository contains supplementary materials for the paper "Blocks? Graphs? Why Not Both? Designing and Evaluating a Hybrid Programming Environment for End-users". We provide this data for transparency reasons and to support replications of our experiemnts. Note: This package is anonymized for peer review purposes. We will provide contact information for the authors at a later date. We also plan to add interactive versions of our tasks and tutorials in an updated version to allow readers easier exploration/experimentation. Summary of files contained in this package This package contains two parts: <ul> <li> The <code>data-analysis/</code> folder contains the raw dataset we collected for our experiment in CSV format, as well as scripts we used for our analyses. <ul> <li>Column <code>ID</code> contains a unique 4-digit identifier for each participant that they were assigned throughout our study.</li> <li>Column <code>Group</code> contains the group (Blocks/Graph) that participants were randomly assigned to.</li> <li>Columns <code>Task1Time</code> and <code>Task2Time</code> contain the time participants spent to complete the two programming tasks of our study in minutes.</li> <li>Columns <code>Task1Success</code> and <code>Task2Success</code> contain a boolean value indicating whether the participants successfully completed the given task. Note that participants had unlimited attempts until they timed out after a strict time limit of 30 minutes, so if a participant was unsuccessful the corresponding time value is 30.</li> <li>Columns <code>Task1Tests</code> and <code>Task2Tests</code> contain the number of times a participant executed their code throughout a task, including their final submission if they were successful.</li> <li>Columns <code>LearnTask</code>, <code>ReadTask</code> and <code>WriteTask</code> contain the scores that participants gave to the task editor component of their assigned programming environment. There are 3 scores for the categories "learnability", "readability" and "writability". Scores are on a 5-point scale from 1 (worst) to 5 (best).</li> <li>Columns <code>LearnTrig</code>, <code>ReadTrig</code> and <code>WriteTrig</code> contain the scores that participants gave to the trigger editor component of their assigned programming environment. There are 3 scores for the categories "learnability", "readability" and "writability". Scores are on a 5-point scale from 1 (worst) to 5 (best).</li> <li>Columns <code>LearnComp</code>, <code>ReadComp</code> and <code>WriteComp</code> contain the scores that participants gave to their assigned assigned programming environment in direct comparison to the other alternative. There are 3 scores for the categories "learnability", "readability" and "writability". Unlike in the paper, where scores are on a scale from -2 to 2, the raw scores here are on a 5-point scale from 1 (strong preference for other environment) to 5 (strong preference for own environment).</li> <li>The script <code>survival.py</code> was used to perform the survival analysis presented in the paper and generate the related figure.</li> <li>The script <code>batplot.py</code> was used to generate the 3x3 grid of ratings used in a figure in the paper.</li> </ul> </li> <li> The <code>materials/</code> folder contains the tutorials and task descriptions we presented to study participants. It also contains the exact wording of pre-screening and post-experiemental survey questions. <ul> <li>The image <code>pre-screening.png</code> shows the three pre-screening questions we used to determine whether our participants could be included in our study.</li> <li>The images <code>tutorial1_instructions.png</code> and <code>tutorial1_sim.png</code> contain the instructions and initial simulator state we provided to participants for the first programming tutorial. This tutorial did not provide starter code and was identical for both participant groups.</li> <li>The images <code>tutorial2_instructions.png</code> and <code>tutorial2_sim.png</code> contain the instructions and initial simulator state we provided to participants for the second programming tutorial. This tutorial was identical for both participant groups and provided participants with starter code, which is shown in the images: <ul> <li><code>tutorial2_code_main.png</code> for the main program in the left canvas</li> <li><code>tutorial2_code_move.png</code> for the definition of "Move box to the right".</li> </ul> </li> <li>The images <code>tutorial3_instructions_blocks.png</code>/<code>tutorial3_instructions_graph.png</code> and <code>tutorial3_sim.png</code> contain the instructions and initial simulator state we provided to participants for the third programming tutorial. This tutorial also provided participants with starter code, which is shown in the images: <ul> <li><code>tutorial3_code_main.png</code> for the main program in the left canvas</li> <li><code>tutorial3_code_pick.png</code> for the definition of "Pick up box"</li> <li><code>tutorial3_code_place.png</code> for the definition of "Place box"</li> </ul> </li> <li>The images <code>task1_instructions.png</code> and <code>task1_sim.png</code> contain the instructions and initial simulator state we provided to participants for the first programming task. The task did not provide starter code and the instructions were identical for both participant groups.</li> <li>The images <code>task2_instructions.png</code> and <code>task2_sim.png</code> contain the instructions and initial simulator state we provided to participants for the second programming task. The instructions were identical for both groups. This task also provided participants with starter code, which is shown in the images: <ul> <li><code>task2_code_main.png</code> for the main program in the left canvas</li> <li><code>task2_code_pick_prog.png</code> for the definition of "Pick up block"</li> <li><code>task2_code_load_trig_blocks.png</code>/<code>task2_code_load_trig_graph.png</code> for the definition of the trigger "Ready to load machine"</li> <li><code>task2_code_load_prog.png</code> for the definition of "Load and activate machine"</li> <li><code>task2_code_finished_trig_blocks.png</code>/<code>task2_code_finished_trig_graph.png</code> for the definition of the trigger "Machine finished"</li> <li><code>task2_code_finished_prog1.png</code> for the definition of "Get block from machine"</li> <li><code>task2_code_finished_prog2.png</code> for the definition of "Place block in bin"</li> </ul> </li> <li>The image <code>usability.png</code> shows the usability questions we used to determine a participant's rating of their assigned programming environment. The questions were identical for both participant groups.</li> <li>The images <code>comprehension_blocks_1.png</code> and <code>comprehension_blocks_2.png</code> show the program comprehension questions we used to determine whether participants in the Blocks group could understand more complex triggers.</li> <li>The images <code>comprehension_graph_1.png</code> and <code>comprehension_graph_2.png</code> show the program comprehension questions we used to determine whether participants in the Graph group could understand more complex triggers.</li> <li>The images <code>comparison_blocks.png</code> and <code>comparison_graph.png</code> show the images of triggers in the alternative environment that we showed to our participants before choosing their preferred environment. The questions were identical for both participant groups.</li> <li>The image <code>comparison.png</code> shows the questions we used to determine a participant's preference between the two programming environment alternatives.</li> </ul> </li> </ul>

Molecular dynamics (MD) simulations methods and results on cyclooctene oxides in ACN/water hybrid electrolytes

Molecular dynamics (MD) simulations methods and extended results used for the Perspective article entitled “Fine tuning of electrosynthesis pathways by modulation of electrolyte solvation structure”

Data for the paper: Towards high solar contribution in hybrid CSP-combined cycle gas turbine plants

Data used for the paper "Towards high solar contribution in hybrid CSP-combined cycle gas turbine plants".

Input-Output Global Hybrid Analysis of Agricultural Primary Production (IO-GHAAP) Database

A commonly used method to examine the relationship between global water consumption and production is input--output analysis. However, between approximately 70% and 90% of freshwater consumption occurs in agricultural primary production, which is often represented by only a small percentage of the total number of sectors in input-output databases. In addition, the assessment of the impact of water consumption is usually carried out at the national level. Therefore, the primary objective of the Input-Output Global Hybrid Analysis of Agricultural Primary Production (IO-GHAAP) approach was to improve assessments of water use and its impacts in input-output analysis. To achieve this objective, a global spatial model of agricultural primary production MapSPAM (IFPRI, 2019) was integrated into the existing input-output database GLORIA (Lenzen et al., 2017, 2021) via prorating. The resulting IO-GHAAPP approach includes (1) a disaggregated input-output database and novel environmental extensions for freshwater consumption and scarcity. The IO-GHAAPP database consists of 150 categories and 164 regions, resulting in a total of 24,600 region-category combinations. Forty-two of the categories are dedicated to agricultural primary production (28%). In comparison, the source input--output data consist of 120 categories and 164 regions, resulting in a total of 19,680 region-category combinations, of which 14 are dedicated to agricultural primary production (12%).   Please cite as: Bunsen, Jonas, Vlad Coroamă, and Matthias Finkbeiner. 2023. ‘Input-Output Global Hybrid Analysis of Agricultural Primary Production (IO-GHAAPP) Database’. Sustainability 15 (2). <a href="https://doi.org/10.3390/su15129351">https://doi.org/10.3390/su15129351</a>.   References: <ul> <li>IFPRI. 2019. ‘Global Spatially-Disaggregated Crop Production Statistics Data for 2010 Version 2.0’. Harvard Dataverse. <a href="https://doi.org/10.7910/DVN/PRFF8V">https://doi.org/10.7910/DVN/PRFF8V</a>.</li> <li>Lenzen, Manfred, Arne Geschke, Muhammad Daaniyall Abd Rahman, Yanyan Xiao, Jacob Fry, Rachel Reyes, Erik Dietzenbacher, et al. 2017. ‘The Global MRIO Lab - Charting the World Economy’. Economic Systems Research 29 (2): 158–86. <a href="https://doi.org/10.1080/09535314.2017.1301887">https://doi.org/10.1080/09535314.2017.1301887</a>.</li> <li>Lenzen, Manfred, Arne Geschke, James West, Jacob Fry, Arunima Malik, Stefan Giljum, Llorenç Milà i Canals, et al. 2021. ‘Implementing the Material Footprint to Measure Progress towards Sustainable Development Goals 8 and 12’. Nature Sustainability, December. <a href="https://doi.org/10.1038/s41893-021-00811-6">https://doi.org/10.1038/s41893-021-00811-6</a>.</li> </ul>

Identification of hybrids between the Japanese giant salamander and Chinese giant salamander using deep learning and smartphone images

Biological invasions are recognized as one of the factors causing biodiversity loss. Incomplete reproductive isolation with a closely related species can result in hybridization when a non-native species is introduced into a new habitat. Management of hybrids is essential for biodiversity conservation; however, the distinction between the two species becomes a challenge in cases of hybrids with similar characteristics to native species. Although image recognition technology can be a powerful tool for identifying hybrids, studies have yet to utilize deep learning approaches. Hence, this study aimed to identify hybrids between native Japanese giant salamanders (Andrias japonicus) and non-native Chinese giant salamanders (Andrias davidianus) using EfficientNet and smartphone images. We used smartphone images of 11 native individuals (with 5 training and 6 test images) and 20 hybrid individuals (with 5 training and 15 test images). In our experimental environment, an AI model constructed with efficientNet-V2 showed 100% accuracy in identifying hybrids. In addition, highlighting the regions that influenced the AI model's predictions using Grad-CAM revealed that salamander head spots are responsible for correctly classifying native and hybrid species. The results of this study revealed that our approach is one of the methods that enable the identification of hybrids, which was previously considered difficult without identification by the experts. Furthermore, since this study achieved high-performance identification using smartphone images, it is expected to be applied to a wide range of low-cost identification using citizen science.

opencc-by-4.0May 2023View details →

Particle filter meets hybrid octrees: an octree-based ground vehicle localization approach without learning

This paper proposes an accurate lidar-based outdoor localization method that requires few computational resources, is robust in challenging environments (urban, off-road, seasonal variations) and whose performances are equivalent for two different sensor technologies: scanning LiDAR and flash LiDAR. The method is based on the matching between a pre-built 3D map and the LiDAR measurements. Our contribution lies in the combined use of a particle filter with a hybrid octree to reduce the memory footprint of the map and significantly decrease the computational load for online localization. The design of the algorithm allows it to run on both CPU and GPU with equivalent performance. We have evaluated our approach on the KITTI dataset and obtained good results compared to the state of the art. This paper introduces the baseline performance on a multi-seasonal dataset we are publicly releasing to the community. We have shown that the same localization algorithms and parameters can perform well in urban environments and can be extended to off-road environments. We have also evaluated the robustness of our method when masking angular sectors of the LiDAR field of view to reproduce edgecases scenarios in urban environments where the LiDAR field is partially occulted by another vehicle (bus, truck). Finally, experiments have been carried out with two distinctive scanning and flash LiDAR technologies. The performance achieved with the flash LiDAR is close to the scanning LiDAR despite different resolutions and sensing modalities. The positioning performance is significant with 10cm and 0.12° angular RMSE for both technologies. We validated our approach in an off-road environment from a front view field of view with only 768 LiDAR points.

opencc-zeroMay 2023View details →

Data from: Developmental rate displays effects of inheritance but not of sex in interpopulation hybrids of Tigriopus californicus

Coevolved genetic interactions within populations can be disrupted by hybridization resulting in loss of fitness in hybrid individuals (i.e., hybrid breakdown). However, the extent to which variation in fitness-related traits among hybrids is inherited across generations remains unclear, and variation in these traits may be sex-specific in hybrids due to differential effects of genetic incompatibilities in females and males. Here we present two experiments investigating variation in developmental rate among reciprocal inter-population hybrids of the intertidal copepod Tigriopus californicus. Developmental rate is a fitness-related trait in this species that is affected by interactions between mitochondrial-encoded and nuclear-encoded genes in hybrids that result in variation in mitochondrial ATP synthesis capacities. First, we show that F2-hybrid developmental rate is equivalent in two reciprocal crosses and is unaffected by sex, suggesting that breakdown of developmental rate is likely experienced equally by females and males. Second, we demonstrate that variation in developmental rate among F3 hybrids is heritable; times to copepodid metamorphosis of F4 offspring of fast-developing F3 parents (12.25 ± 0.05 d, μ ± SEM) were significantly faster than those of F4 offspring of slow-developing parents (14.58 ± 0.05 d). Third, we find that ATP synthesis rates in these F4 hybrids are unaffected by the developmental rates of their parents, but that mitochondria from females synthesize ATP at faster rates than mitochondria from males. Taken together, these results suggest that sex-specific effects vary among fitness-related traits in these hybrids and that effects likely associated with hybrid breakdown display substantial inheritance across hybrid generations.

opencc-zeroMay 2023View details →

Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, with insights into the complex biogeographic history in the Northern Hemisphere

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In this study, 785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian-western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming datasets.

The Friction of radially loaded hybrid spindle bearings under high speeds

Friction losses are an important parameter for evaluating the operational behaviour of high-speed rolling bearings. Especially in machine tool applications, the bearings are subjected to high radial loads, which lead to increased forces in the rolling contact and thus to increased bearing friction. At high speeds, hybrid spindle bearings are typically used, consisting of ceramic balls and steel raceways, which are characterised by better frictional behaviour compared to steel bearings. A precise knowledge of the friction characteristics, especially at high speeds, makes it possible to improve friction models and to extrapolate them to spindle bearings of other types and sizes, geometries and other operational conditions. In the following article, a new straight forward method to measure the frictional torque in spindle bearings is presented. A rigidly arranged hybrid spindle bearing pair of the type 7008 was tested over varying speeds and radial loads evaluated in a characteristic diagram. The influence of oil air and grease lubrication was investigated. Based on the test parameters, a current friction calculation  method was presented and validated. The influence of outer race control and minimized power dissipation is discussed.

opencc-by-4.0May 2023View details →

Data and code example for the article: "Massively parallel hybrid quantum-classical machine learning for kernelized time-series classification"

Data needed to reproduce the figures of <a href="https://arxiv.org/abs/2305.05881">https://arxiv.org/abs/2305.05881</a> and a simple code example of a quantum-convex-classical neural network used to train a sine versus cosine classification problem.

opencc-zeroJun 2023View details →

Podarcis bocagei vs P. carbonelli hybrid zone SNP datasets from ddRADseq

We used double digestion restriction site associated DNA (ddRAD) sequencing to discover SNPs in samples across a transect including a hybrid zone between Podarcis carbonelli and Podarcis carbonelli. We used P. bocagei and P. carbonelli samples from the locations at the extremes of the transect as references. We obtained a SNP dataset including all SNPs after removing loci with depth coverage <8, missing data >20%, removing loci containing more than five SNPs, and with more than 70% heterozygosity (complete dataset; 6905 SNPs, 329 individuals). Additionally, we obtained from the complete dataset two other datasets, prior to apply a missing data filter. One dataset contained loci with allele frequencies higher than 0.8 in the reference population containing only parental individuals of one species and lower than 0.2 in the reference population of the other species ("80/20" dataset; 2300 SNPs, 329 individuals); the other dataset comprised diagnostic SNPs between reference populations (diagnostic dataset; 1241 SNPs, 236 individuals) but excluding private alleles from references, i.e. excluding alleles that are not present in the populations of contact. Individuals with missing data >35% were removed from all datasets (the number of individuals reported for each dataset is after applying this filter, but note that the 80/20 and the diagnostic datasets were obtained before applying this filter to the complete dataset). Across datasets, average depth of coverage by individuals was 28 (median = 26.8, min = 12.5, max = 85.8) and by loci was 29 (median = 28.8; min = 15.6; max = 48.6). The analysis of replicate samples (four samples were replicated twice, i.e. were amplified and sequenced in independent libraries and SNP calling was performed independently) showed high levels (99.87%) of multilocus genotype replicability.

opencc-by-4.0May 2023View details →

Making andesite through shallow hybridization of magmas derived from variably enriched lithospheric mantle

We integrate textural and in situ compositional information from plagioclase and clinopyroxene (Cpx) phenocrysts together with groundmass compositions in early Cretaceous andesite dykes within the Sulu belt of China to propose a new petrogenetic model for andesite. Plagioclase phenocrysts are mostly andesine; they are depleted in high field strength elements (HFSE). However, clinopyroxene (Cpx) phenocrysts are either reversely-zoned (type I) or homogeneous (type II), with the zoned Cpx divided into subtypes IA and IB. All Cpx has high Mg#, low Na2O and generally low Al2O3, with depletions in HFSE and variably high 87Sr/86Sr ratios, suggesting crystallization above the Moho from magmas derived from enriched lithospheric mantle. The cores of type IA/IB and type II Cpx have normal major- and trace-element compositional variations and similar 87Sr/86Sr ratios to each other and to plagioclase, consistent with fractional crystallization from a common magma (magma 1). The rims of type IA and IB Cpx also have normal major- and trace-element compositional variations, but these are not as evolved as the cores, and the rims have lower 87Sr/86Sr ratios, demonstrating crystallization from an isotopically-distinct magma (magma 2). Based on modelled major and rare earth element compositions of magmas inferred to have been in equilibrium with different Cpx (± plagioclase) domains, the measured groundmass compositions can be reproduced by variable mixing between the two magmas. Our study demonstrates for the first time that andesite magma can be made through fractionation and shallow hybridization of magmas derived from variably enriched lithospheric mantle.

opencc-zeroJun 2023View details →

Data from: Limited, asymmetric hybridization between coastal cutthroat trout and steelhead in a Northern California river

Hybridization between coastal cutthroat trout (Oncorhynchus clarkii clarkii) and steelhead (O. mykiss) was assessed in the Smith River, California. Individuals were categorized as pure or as one of 10 hybrid classes using 30 'diagnostic' single-nucleotide polymorphisms positioned on 26 separate chromosomes. Most of the individuals examined (n = 876), were pure coastal cutthroat trout (n = 634) or pure steelhead (n = 213), and 29 individuals were identified as having hybrid ancestry. Among hybrids, first generation hybrids (n = 15) and coastal cutthroat trout backcrosses (n = 12) were the most common. No individuals were identified as backcrosses to SH, suggesting the presence of genetic or behavioral mechanisms constraining such backcrosses, or the growth and survival of their progeny. Mitochondrial DNA of 14 of 15 F1 hybrids was of steelhead origin, suggesting that hybridization was driven primarily by sneak-mating of male coastal cutthroat trout with female steelhead. Evaluation of classical phenotypic characters for coastal cutthroat trout and steelhead (i.e., jaw slash, maxillary length, and hyoid teeth) were not reliable by themselves for identification of either pure parental fish or hybrids. In contrast, analysis with geometric morphometrics revealed distinctive body shapes for pure coastal cutthroat trout and steelhead, and the combination of classical traits and geometric morphology was mostly accurate in distinguishing them. However, first generation hybrids and backcrosses overlapped completely with parental types, highlighting challenges in hybrid identification using phenotypic traits.

opencc-zeroDec 2022View details →

Phylogenomics reveals patterns ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives

Despite the economic, ecological, and scientific importance of the genera Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens) Salicaceae, we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees. Salix subgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a 'spectacular failure' due to a speculated radiation of the subgenera Vetrix and Chamaetia. Here we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed polyphyly of others. Using an fbranch analysis we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of the Vetrix-Chamaetia clade in Salix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in both Salix and Populus have played important roles in the diversification and diversity in these two genera.

opencc-zeroJun 2023View details →

Data for: Positive in situ hybridization for ZIKV RNA in MFI tissues and gravid uteri slides

Zika virus (ZIKV) can be transmitted vertically from mother to fetus during pregnancy, resulting in a range of outcomes, including severe birth defects and fetal/infant death. Potential pathways of vertical transmission in utero have been proposed but remain undefined. Identifying the timing and routes of vertical transmission of ZIKV may help us identify when interventions would be most effective. Furthermore, understanding what barriers ZIKV overcomes to effect vertical transmission may help improve models for evaluating infection by other pathogens during pregnancy. The images included in this dataset belong to a study that aimed to determine the pathways of vertical transmission using a rhesus macaque model. Pregnant rhesus macaques were inoculated with 104 plaque forming using (PFA) of an African-lineage ZIKV isolate (ZIKV-DAK) at gestational day 30 (term is 165 days). Maternal-fetal interface and gravid uteri were evaluated for ZIKV RNA using in situ hybridization (ISH). The included images are the maternal fetal interface tissues and coronal sections evaluated for ZIKV via ISH, areas were ZIKV RNA was detected have pink/red staining. The pattern of infection observed in the maternal-fetal interface provides evidence of vertical ZIKV transmission through the fetal membranes.